Materials for Biocomputing Course, Spring 2015
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README.md
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README.md

UTbiocomputing2015

Peer-led working group in Biological Computing at UT Austin, Spring 2015

Rebecca Tarvin (PAT 123) rdtarvin@utexas.edu
Stephanie Spielman (MBB 3.232) stephanie.spielman@gmail.com

Open Coding Hour: Tuesdays 5-6pm in CCBB conference room (GDC 7.514)
Class: 4-5pm on Wednesdays in FNT 1.104

New class website: http://sjspielman.org/UTbiocomputing2015/
Class website: https://github.com/sjspielman/UTbiocomputing2015
Resources: https://github.com/sjspielman/UTbiocomputing2015/blob/master/resources.md

The goal of this class is to take away any fear of programming that you may have so that computing can become an advantage rather than a barrier to your research. On Wednesdays, we will provide lessons suitable for beginners in programming. Each week you should post at least one question and answer on the google group (UTbiocomputing, http://goo.gl/PLnSpP) and complete the homework. On Tuesdays we will help you with homework or if you had no problems, come anyways to meet other people that are computing at UT, and get some handy tips from GSAF's Scott Hunicke-Smith.

Please install the required software no later than the second day of class. Here are some recommended resources for all your computing needs. The resources are not required reading, but they are tremendously useful!

A new and awesome resource: Rosetta Code !!!!!

Another new and awesome resource, sponsored by UT! http://www.lynda.com/ .

To download files (pdf, csv, or text), try viewing in Raw format.

Course Schedule

Week Calendar Date Topic Description Teacher
WEEK 00 Jan 21 Introduction Welcome! Becca
WEEK 01 Jan 28 Unix/Bash Basic commands Becca
WEEK 02 Feb 04 Python 1 When to use & basic structure Stephanie
WEEK 03 Feb 11 Python 2 Control flow and loops (if, for, while) Becca
WEEK 04 Feb 18 Python 3 Functions Stephanie
WEEK 05 Feb 25 Python 4 File Input & Output Stephanie
WEEK 06 Mar 04 Python 5 Testing Becca
WEEK 07 Mar 11 Python 6 Numpy & Biopython Stephanie
SPRING BREAK Mar 18 Spring break WOOO! Everybody!
WEEK 08 Mar 25 PyBash Merging Python and Unix/Bash Stephanie and Becca
WEEK 09 Apr 01 git Collaboration and version control slides Cheng Lee
WEEK 10 Apr 08 R Statistical analyses Nathan Pope
WEEK 11 Apr 15 pandas data analysis in python Ben Liebeskind
WEEK 12 Apr 22 TACC Using high-performance computing systems Benni Goetz
WEEK 13 Apr 29 RNAseq Computational platforms and pipeline slides Dariya Sydykova
WEEK 14 May 06 pyRAD pipeline for analyzing NextGen SNP data April Wright